The present invention relates to novel nucleosides and oligonucleotides having conformationally constrained sugar moieties.
Nucleosides derived from natural D-ribose play a significant role for the treatment of human viral diseases, neoplastic diseases, and modulation of immune response. Among them, Ribavirin (1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide), AZT (3xe2x80x2-azido-3xe2x80x2-deoxythymidine), ddI (2xe2x80x2,3xe2x80x2-dideoxyinosine), and ddC (2xe2x80x2,3xe2x80x2-dideoxycytidine) are among the most prominent drugs presently approved. Despite their relatively potent antiviral and antineoplastic activity, emerging resistance of many viruses and tumor cells prompted a search for new nucleosides.
In addition to nucleosides derived from D-ribose, novel nucleosides employing sugars in L-conformation have been proposed as antiviral agents, and several L-nucleosides appear to have significant biological activity at lower toxicity than their counterpart D-nucleosides. The most active L-nucleosides reported to date include L-T (L-thymidine), 3TC (L-3xe2x80x2-thiacytidine), FTC (L-5-fluoro-3xe2x80x2-thiacytidine), L-ddC (L-2xe2x80x2,3xe2x80x2-dideoxycytidine), and L-FddC (L-5-fluoro-2xe2x80x2,3xe2x80x2-dideoxycytidine).
Furthermore, variations of D-nucleosides with novel sugar and sugar-like rings have been developed by introducing different heterocyclic moieties. For example, the replacement of a furanose ring with 1,3-dioxolane, 1,3-oxathiolane, 4xe2x80x2-thio heterocylic moieties has produced potent anti-viral compounds. Nucleosides containing tetrahydrothiophene, isoxazole, oxazolidine, thiazolidine and pyrrolidine ring systems instead of D-ribose are also known. Furthermore, an L-nucleoside analog (3TC) containing a non-ribose heterocyclic moiety has been approved for the treatment of human immunodeficiency virus (HIV) replication and hepatitis B virus (HBV) propagation.
More recently, bicyclic D-nucleosides have been prepared and found to be inhibitors of HIV reverse transcriptase [V. E. Marquez et al., J. Med. Chem., 20, 2780-2789, 1998]. Additionally, bicyclic D-nucleosides have been incorporated into oligonucleotide sequences and screened as anti-sense agents [S. Obika et al., Tetrahedron Letts, 39, 5401-5404, 1998]. Wengel and Nielsen described in their international patent application WO 99/14226 oligonucleotides with bicyclic D-nucleotides having additional rings in various positions.
There are, however, no reports on conformationally constrained bi-, and tricyclic L-nucleosides. Therefore, there is a need to provide methods and compounds for conformationally constrained bi-, and tricyclic L-nucleosides.
The present invention is directed to conformationally constrained L-nucleosides of the general structure as shown below. 
The nucleobase generally includes natural and non-natural bases, and the L-sugar includes a natural or non-natural sugar in L-configuration having at least one additional cyclic structure (i.e., ring) formed by a bridge having the general structure Axe2x80x94Bxe2x80x94Z. An optional connector moiety may be covalently bound to the L-sugar, and where a connector moiety is present, the connector and the nucleobase are separated by at least one atom in the sugar. While in some preferred conformationally constrained L-nucleosides a single additional ring is formed by bridging the C1-C4, C1-C2, C1-C3, C2-C4, or C3-C4 atoms, other nucleosides may have two additional rings by bridging both the C1-C2, and the C3-C4 atoms, or both the C1-C3 and the C2-C4 atoms.
In one aspect of the inventive subject matter, the conformationally constrained nucleosides have a structure as generally depicted in Structures I-IX. The Base is a nucleobase covalently bound to the C1-atom via a nitrogen- or carbon atom in the nucleobase and is preferably a substituted or unsubstituted purine or pyrimidine base, a substituted or unsubstituted imidazole, pyrazole, pyrrole, or triazole. X is typically oxygen, but may also be substituted with alternative heteroatoms, including substituted and unsubstituted sulfur, nitrogen, carbon, and selenium. In structure IV, E, F, and G are typically xe2x80x94CH2xe2x80x94 or xe2x80x94C(H)(OH)xe2x80x94, and the bridge elements A, B, and Z are independently substituted or unsubstituted carbon, lower (i.e., with up to 5 carbon atoms) branched or unbranched alkyl or alkenyl, or substituted or unsubstituted heteroatoms, including oxygen, sulfur, and nitrogen. Contemplated optional connectors include bi- and multifunctional groups such as mono-, di-, and triphosphate groups, diacids, diamides, etc., and are preferably covalently connected to any one of R1-R4, A, B, and Z. R1-R4 are independently nothing, H, OH, substituted and unsubstituted sulfur, nitrogen, carbon or phosphorus. Depending on the individual substituents, the conformationally constrained L-nucleoside may be electrically neutral, charged or in a salt form with an appropriate salt. 
In more preferred aspects of structures I-IX, X is O, S. CHOH, CH2 or Nxe2x80x94COCH3, A is O, S, (CH2)n, Nxe2x80x94R, or nothing, and B and Z are independently O, S, (CH2)n, or Nxe2x80x94R. When both B and Z are independently O, S or Nxe2x80x94R then A is (CH2)n, and when both A and B are independently O, S or Nxe2x80x94R then Z is (CH2)n, wherein R is H, OH, COxe2x80x94, lower alkyl or COCH3, and n is 1-5. It is also preferred that no more than two of A, B, and Z are an atom other than a carbon atom. R2 and R3 are independently H, OH, OPO32xe2x88x92, CN, halogen, N3, CH2OH, methylidene, lower alkyl or lower alkyl amine, and R1 and R4 is H, OH, OPO32xe2x88x92. In structure IV, E is preferably O, S, (CH2)n, Nxe2x80x94R, or nothing, and F and G are independently O, S, (CH2)n, or Nxe2x80x94R. When both F and G are independently O, S or Nxe2x80x94R then E is (CH2)n, and when both E and F are independently O, S or Nxe2x80x94R then G is (CH2)n, wherein R is H, OH, COxe2x80x94, lower alkyl or COCH3, and n is 1-5; and wherein no more than two of E, F, and G are an atom other than a carbon atom. In both general and preferred structures I-IX, all structures are excluded in which the nucleobase or any of the substituents A, B, Z, X, and R1-R4 are in charge, sterical, stereoelectronic or other structural conflict.
In another aspect of the inventive subject matter, nucleosides according to structures II and III may have only one additional ring in which a bridge of the general structure xe2x80x94Axe2x80x94Bxe2x80x94Zxe2x80x94 covalently connects the carbon atoms C1 and C2, or C3 and C4 in structure II, or carbon atoms C1 and C3, or C2 and C4 in structure III. Where nucleosides according to structure III have only a single additional ring, it is preferred that A and Z are nothing and B is a methylene group.
In a further aspect of the inventive subject matter, the nucleoside is covalently coupled to at least one nucleotide to form a modified oligonucleotide or modified dinucleotide. Although preferred nucleosides have an L-configuration, alternative nucleosides may also have a D-configuration.
Various objects, features, aspects and advantages of the present invention will become more apparent from the following detailed description of preferred embodiments of the invention, along with the accompanying drawing.